Nucleotides Notes Biophysics & Biochemistry
Page 1 of 18
Poly nucleotides
RNA
May Or Not acts like genetic
material
DNA
99.99...% Acts as a
Genetic Material
Acts as a genegtic
Material eg.Virions ^ RNA
viruses
Non Genetic
Ctalytic
eg.Ribozymes (RNA
+Catlyst)
Non Catalytic
Coding
mRNA
Non Coding
tRNA ,SnRNA ,Sno RNA , Si
RNA ,mi RNA , xist etc
Nucleic Acids & Nucleotides
Nucleotides Notes Biophysics & Biochemistry
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Nucleotides
Nucleocide
Sugar Nitrogenous Base
Phosphate Group
PO4
2-
Polymeric form of nucleotides consists of monomeric units Nucleotides
Sugars
• Pentose Sugar
• Cyclic in nature
• Furanose in nature
• 𝜷 𝑺𝒖𝒈𝒂𝒓
• Dipol molecule
Nucleotides Notes Biophysics & Biochemistry
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• Non Planer (Sugar Puckering)
• Opical Activity
Nitrogenous base
• Heterocyclic
• Non- Poalr
• Non Planer
• Non Water soluble
• Two types
• Aromatic
• Absorb radiation due to Pi delocalized electron of aromatic ring (A260nm )
Nucleotides Notes Biophysics & Biochemistry
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Nitrogenouse Base
Purine (PuGA) Double ring
1:9 members in the ring
(Imidazole)
Pyrimidine (PyCUT )
Single ring
Adeninie
6-Amino purine
Guanin
6-Oxy-2
aminopurine
Cytosine
4-Amino-2-Oxy-
pyridine
Uracil
4,2-dioxy
pyridine
Thymine(5-
methyle Uracil)
5-methyle-4,2-
dioxy pyridine
Nucleotides Notes Biophysics & Biochemistry
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Effects of pH on bases
Nucleotides Notes Biophysics & Biochemistry
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In case of bases the order of protonation in the bases when pH moves ph7 to pH3
N1 > N7 >N3
Bases after Protonation
Common Form Rare Form
Amino form to Imino
form
Common to rare is called
Tautomeric shift
A (Amino) –NH2 A (Imino) –NH
C (Amino) –NH2 C (Imino) –NH
G Keto >C=O G (Enol)}C-OH
T Keto >C=O T (Enol)}C-OH
Nucleotides Notes Biophysics & Biochemistry
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Bases Pairing
Common Base Pairing Un- Common (Rare)Base Pairing
𝐴 = 𝑇 𝐴 = 𝐶
𝑇 = 𝐴 𝐶 = 𝐴
𝐺 ≡ 𝐶 𝐺 ≡ 𝑇
𝐶 ≡ 𝐺 𝑇 ≡ 𝐺
De amination of Nitrogenous Bases Removal of Amine group
𝐴 − − − −→ 𝐻𝑦𝑝𝑜𝑥𝑎𝑛𝑡ℎ𝑖𝑛𝑒
𝐺 − − − −→ 𝑋𝑎𝑛𝑡ℎ𝑖𝑛𝑒
𝐶 − − − −→ 𝑈𝑟𝑎𝑐𝑖𝑙
5, 𝑚𝑒𝑡ℎ𝑦𝑙𝑒 𝑐𝑦𝑡𝑜𝑐𝑖𝑛𝑒 − − − −→ 𝑇ℎ𝑦𝑚𝑖𝑛𝑒
Nucleoside
Nucleotides Notes Biophysics & Biochemistry
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Nucleotides Notes Biophysics & Biochemistry
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Isomers in Nitrogenous Bases
Anti conformation is more suitable while syn is less because of steric clash or hindrance made
bond unstable
Nucleotides Notes Biophysics & Biochemistry
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BIOLOGICAL FUNCTIONS OF NUCLEOTIDES
Nucleotides Notes Biophysics & Biochemistry
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· Precursors of DNA and RNA.
· Activated intermediates in many biosynthesis: e.g UDP-glucose ® glycogen,
diacylglycerol ® phosphoglycerates, S-adenosylmethionine as methyl donor, etc.
· Nucleoside triphosphates, especially ATP, as the universal currency of energy in biological systems.
· Adenine nucleotides are components of the coenzymes, NAD(P)+
, FAD, and CoA.
· Metabolic regulators: (a) c-AMP is the mediator of hormonal actions; (b) ATP-dependent protein
phosphorylation - activates phosphorylase and inactivates glycogen synthase; (c) adenylation of a Tyr of
bacterial glutamine synthetase - more sensitive to feedback inhibition and less active; (d) allosteric
regulator - glycogen phosphorylase activated by ATP and inactivated by AMP.
Inosine
Nucleoside sugar base with hypoxanthine (De – aminated adenine)
Nucleotides Notes Biophysics & Biochemistry
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AMP(Adenosine Mono phosphate)
𝑨𝒅𝒊𝒏𝒊𝒏𝒆 + 𝑺𝒖𝒈𝒂𝒓 + 𝒔𝒊𝒏𝒈𝒍𝒆 𝑷𝒉𝒐𝒔𝒑𝒉𝒂𝒕𝒆 = 𝐀𝐌𝐏
ADP (Adenosine Di phosphate)
Nucleotides Notes Biophysics & Biochemistry
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ATP (Adenosine Tri Phosphate)
Nucleotides Notes Biophysics & Biochemistry
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Active form of ATP ATP+Mg +2
OR Mn+2
ATP = ADP +Pi (Orthophosphate) + -7.3Kcal/mol or ∆𝑮𝒐𝟏
ATP = AMP +PPi (Pyrophosphate) + -7.8Kcal/mol or ∆𝑮𝒐𝟏
Total 7.3+7.8=≈ −𝟏𝟒
PPi=2Pi + -8Kcal/Mol
So total 20 Kcal/Mol of ATP
NAD+
Nicotinamide adenine dinucleotide (
Coenzyme)
• Oxidizing agent
• In oxidized form
• Electron acceptor
Nucleotides Notes Biophysics & Biochemistry
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NADH (Nicotinamide adenine dinucleotide)
NAD+
+2e-
+H+
=NADH
• Reducing agent
• In Reduced form
• Electron donor
Nucleotides Notes Biophysics & Biochemistry
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FAD (Flavin adenine dinucleotide)
• Oxidizing agent
• In oxidized form
• Electron acceptor
FADH2 (FAD + 2e-
+2H)
• Reducing agent
• In Reduced form
Nucleotides Notes Biophysics & Biochemistry
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• Electron donor
FMN (Flavin mono nucleotide ) also called Pseudo nucleotide
B2(Isoalloxazine ring +Ribito )+Phosphate = FMN
FMN+AMP=Flavin adenine di nucleotide
cAMP
• Acts as a secondary messenger
• Intracellular signal molecule
• Hydrophilic in nature
ATP ( Adenylate cyclase )
Nucleotides Notes Biophysics & Biochemistry
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Importance of Nucleotides
• The nucleotides are of great importance to living organisms, as they are the building blocks of nucleic
acids, the substances that control all hereditary characteristics.
• In the two families of nucleic acids, ribonucleic acid (RNA) and deoxyribonucleic acid (DNA), the
sequence of nucleotides in the DNA or RNA codes for the structure of proteins synthesized in the cell.
• The nucleotide adenosine triphosphate (ATP) supplies the driving force of many metabolic processes.
Several nucleotides are coenzymes; they act with enzymes to speed up (catalyze) biochemical reactions.
• Nucleosides are similar to nucleotides except that they lack the phosphate group. Nucleosides themselves
rarely participate in cell metabolism.
• Adenosine monophosphate (AMP) is one of the components of RNA and also the organic component of
the energy-carrying molecule ATP. In certain vital metabolic processes, AMP combines with inorganic
phosphate to form ADP (adenosine diphosphate) and then ATP. The breaking of the phosphate bonds in
ATP releases great amounts of energy that are consumed in driving chemical reactions or contracting
muscle fibers. Cyclic AMP, another nucleotide, is involved in regulating many aspects of cellular
metabolism, such as the breakdown of glycogen.
• A dinucleotide, nicotinamide adenine dinucleotide (NAD), participates in many oxidation reactions as an
electron carrier, along with the related compound nicotinamide adenine dinucleotide phosphate (NADP).
These substances act as cofactors to certain enzymes.

Nucleotides & Nucleic Acids Notes for Biophysics and Biochemistry

  • 1.
    Nucleotides Notes Biophysics& Biochemistry Page 1 of 18 Poly nucleotides RNA May Or Not acts like genetic material DNA 99.99...% Acts as a Genetic Material Acts as a genegtic Material eg.Virions ^ RNA viruses Non Genetic Ctalytic eg.Ribozymes (RNA +Catlyst) Non Catalytic Coding mRNA Non Coding tRNA ,SnRNA ,Sno RNA , Si RNA ,mi RNA , xist etc Nucleic Acids & Nucleotides
  • 2.
    Nucleotides Notes Biophysics& Biochemistry Page 2 of 18 Nucleotides Nucleocide Sugar Nitrogenous Base Phosphate Group PO4 2- Polymeric form of nucleotides consists of monomeric units Nucleotides Sugars • Pentose Sugar • Cyclic in nature • Furanose in nature • 𝜷 𝑺𝒖𝒈𝒂𝒓 • Dipol molecule
  • 3.
    Nucleotides Notes Biophysics& Biochemistry Page 3 of 18 • Non Planer (Sugar Puckering) • Opical Activity Nitrogenous base • Heterocyclic • Non- Poalr • Non Planer • Non Water soluble • Two types • Aromatic • Absorb radiation due to Pi delocalized electron of aromatic ring (A260nm )
  • 4.
    Nucleotides Notes Biophysics& Biochemistry Page 4 of 18 Nitrogenouse Base Purine (PuGA) Double ring 1:9 members in the ring (Imidazole) Pyrimidine (PyCUT ) Single ring Adeninie 6-Amino purine Guanin 6-Oxy-2 aminopurine Cytosine 4-Amino-2-Oxy- pyridine Uracil 4,2-dioxy pyridine Thymine(5- methyle Uracil) 5-methyle-4,2- dioxy pyridine
  • 5.
    Nucleotides Notes Biophysics& Biochemistry Page 5 of 18 Effects of pH on bases
  • 6.
    Nucleotides Notes Biophysics& Biochemistry Page 6 of 18 In case of bases the order of protonation in the bases when pH moves ph7 to pH3 N1 > N7 >N3 Bases after Protonation Common Form Rare Form Amino form to Imino form Common to rare is called Tautomeric shift A (Amino) –NH2 A (Imino) –NH C (Amino) –NH2 C (Imino) –NH G Keto >C=O G (Enol)}C-OH T Keto >C=O T (Enol)}C-OH
  • 7.
    Nucleotides Notes Biophysics& Biochemistry Page 7 of 18 Bases Pairing Common Base Pairing Un- Common (Rare)Base Pairing 𝐴 = 𝑇 𝐴 = 𝐶 𝑇 = 𝐴 𝐶 = 𝐴 𝐺 ≡ 𝐶 𝐺 ≡ 𝑇 𝐶 ≡ 𝐺 𝑇 ≡ 𝐺 De amination of Nitrogenous Bases Removal of Amine group 𝐴 − − − −→ 𝐻𝑦𝑝𝑜𝑥𝑎𝑛𝑡ℎ𝑖𝑛𝑒 𝐺 − − − −→ 𝑋𝑎𝑛𝑡ℎ𝑖𝑛𝑒 𝐶 − − − −→ 𝑈𝑟𝑎𝑐𝑖𝑙 5, 𝑚𝑒𝑡ℎ𝑦𝑙𝑒 𝑐𝑦𝑡𝑜𝑐𝑖𝑛𝑒 − − − −→ 𝑇ℎ𝑦𝑚𝑖𝑛𝑒 Nucleoside
  • 8.
    Nucleotides Notes Biophysics& Biochemistry Page 8 of 18
  • 9.
    Nucleotides Notes Biophysics& Biochemistry Page 9 of 18 Isomers in Nitrogenous Bases Anti conformation is more suitable while syn is less because of steric clash or hindrance made bond unstable
  • 10.
    Nucleotides Notes Biophysics& Biochemistry Page 10 of 18 BIOLOGICAL FUNCTIONS OF NUCLEOTIDES
  • 11.
    Nucleotides Notes Biophysics& Biochemistry Page 11 of 18 · Precursors of DNA and RNA. · Activated intermediates in many biosynthesis: e.g UDP-glucose ® glycogen, diacylglycerol ® phosphoglycerates, S-adenosylmethionine as methyl donor, etc. · Nucleoside triphosphates, especially ATP, as the universal currency of energy in biological systems. · Adenine nucleotides are components of the coenzymes, NAD(P)+ , FAD, and CoA. · Metabolic regulators: (a) c-AMP is the mediator of hormonal actions; (b) ATP-dependent protein phosphorylation - activates phosphorylase and inactivates glycogen synthase; (c) adenylation of a Tyr of bacterial glutamine synthetase - more sensitive to feedback inhibition and less active; (d) allosteric regulator - glycogen phosphorylase activated by ATP and inactivated by AMP. Inosine Nucleoside sugar base with hypoxanthine (De – aminated adenine)
  • 12.
    Nucleotides Notes Biophysics& Biochemistry Page 12 of 18 AMP(Adenosine Mono phosphate) 𝑨𝒅𝒊𝒏𝒊𝒏𝒆 + 𝑺𝒖𝒈𝒂𝒓 + 𝒔𝒊𝒏𝒈𝒍𝒆 𝑷𝒉𝒐𝒔𝒑𝒉𝒂𝒕𝒆 = 𝐀𝐌𝐏 ADP (Adenosine Di phosphate)
  • 13.
    Nucleotides Notes Biophysics& Biochemistry Page 13 of 18 ATP (Adenosine Tri Phosphate)
  • 14.
    Nucleotides Notes Biophysics& Biochemistry Page 14 of 18 Active form of ATP ATP+Mg +2 OR Mn+2 ATP = ADP +Pi (Orthophosphate) + -7.3Kcal/mol or ∆𝑮𝒐𝟏 ATP = AMP +PPi (Pyrophosphate) + -7.8Kcal/mol or ∆𝑮𝒐𝟏 Total 7.3+7.8=≈ −𝟏𝟒 PPi=2Pi + -8Kcal/Mol So total 20 Kcal/Mol of ATP NAD+ Nicotinamide adenine dinucleotide ( Coenzyme) • Oxidizing agent • In oxidized form • Electron acceptor
  • 15.
    Nucleotides Notes Biophysics& Biochemistry Page 15 of 18 NADH (Nicotinamide adenine dinucleotide) NAD+ +2e- +H+ =NADH • Reducing agent • In Reduced form • Electron donor
  • 16.
    Nucleotides Notes Biophysics& Biochemistry Page 16 of 18 FAD (Flavin adenine dinucleotide) • Oxidizing agent • In oxidized form • Electron acceptor FADH2 (FAD + 2e- +2H) • Reducing agent • In Reduced form
  • 17.
    Nucleotides Notes Biophysics& Biochemistry Page 17 of 18 • Electron donor FMN (Flavin mono nucleotide ) also called Pseudo nucleotide B2(Isoalloxazine ring +Ribito )+Phosphate = FMN FMN+AMP=Flavin adenine di nucleotide cAMP • Acts as a secondary messenger • Intracellular signal molecule • Hydrophilic in nature ATP ( Adenylate cyclase )
  • 18.
    Nucleotides Notes Biophysics& Biochemistry Page 18 of 18 Importance of Nucleotides • The nucleotides are of great importance to living organisms, as they are the building blocks of nucleic acids, the substances that control all hereditary characteristics. • In the two families of nucleic acids, ribonucleic acid (RNA) and deoxyribonucleic acid (DNA), the sequence of nucleotides in the DNA or RNA codes for the structure of proteins synthesized in the cell. • The nucleotide adenosine triphosphate (ATP) supplies the driving force of many metabolic processes. Several nucleotides are coenzymes; they act with enzymes to speed up (catalyze) biochemical reactions. • Nucleosides are similar to nucleotides except that they lack the phosphate group. Nucleosides themselves rarely participate in cell metabolism. • Adenosine monophosphate (AMP) is one of the components of RNA and also the organic component of the energy-carrying molecule ATP. In certain vital metabolic processes, AMP combines with inorganic phosphate to form ADP (adenosine diphosphate) and then ATP. The breaking of the phosphate bonds in ATP releases great amounts of energy that are consumed in driving chemical reactions or contracting muscle fibers. Cyclic AMP, another nucleotide, is involved in regulating many aspects of cellular metabolism, such as the breakdown of glycogen. • A dinucleotide, nicotinamide adenine dinucleotide (NAD), participates in many oxidation reactions as an electron carrier, along with the related compound nicotinamide adenine dinucleotide phosphate (NADP). These substances act as cofactors to certain enzymes.